mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999160755 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970217)
known disease mutation: rs17622 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:42693953G>AN/A show variant in all transcripts IGV

HGNC symbol

CAPN3

Ensembl transcript ID

ENST00000349748

Genbank transcript ID

NM_173087

UniProt peptide

P20807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1325G>A
cDNA.1546G>A
g.53653G>A

AA changes

R442Q Score: 43 explain score(s)

position(s) of altered AA
if AA alteration in CDS

442

frameshift

known variant

Reference ID: rs121434548

database	homozygous (A/A)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	7	7

known disease mutation: rs17622 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970217)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970217)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970217)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gabp, Transcription Factor, Gabp TF binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.181	0.996
	5.734	1
(flanking)	0.594	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	53651	wt: 0.9683 / mu: 0.9814 (marginal change - not scored)	wt: AACCGGCGGAAGGAC mu: AACCGGCAGAAGGAC	CCGG\|cgga
Donor increased	53650	wt: 0.32 / mu: 0.37	wt: GAACCGGCGGAAGGA mu: GAACCGGCAGAAGGA	ACCG\|gcgg
Donor gained	53649	0.40	mu: AGAACCGGCAGAAGG	AACC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

442

mutated

all conserved

442

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

490

Fcatus

all identical

ENSFCAG00000018326

363

Mmusculus

all identical

ENSMUSG00000079110

490

Ggallus

all identical

ENSGALG00000009050

483

Trubripes

all identical

ENSTRUG00000006900

446

Drerio

all identical

ENSDARG00000041864

426

Dmelanogaster

all identical

FBgn0025866

635

Celegans

all identical

C06G4.2

690

Xtropicalis

all identical

ENSXETG00000012304

383

protein features

start (aa)	end (aa)	feature	details
418	586	REGION	Domain III.	lost
587	649	REGION	Linker.	might get lost (downstream of altered splice site)
649	683	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
650	821	REGION	Domain IV.	might get lost (downstream of altered splice site)
692	725	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
705	716	CA_BIND	1 (Probable).	might get lost (downstream of altered splice site)
722	757	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)
735	746	CA_BIND	2 (Probable).	might get lost (downstream of altered splice site)
787	821	DOMAIN	EF-hand 4.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2190 / 2190

position (AA) of stopcodon in wt / mu AA sequence

730 / 730

position of stopcodon in wt / mu cDNA

2411 / 2411

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

222 / 222

chromosome

strand

last intron/exon boundary

2385

theoretical NMD boundary in CDS

2113

length of CDS

2190

coding sequence (CDS) position

1325

cDNA position
(for ins/del: last normal base / first normal base)

1546

gDNA position
(for ins/del: last normal base / first normal base)

53653

chromosomal position
(for ins/del: last normal base / first normal base)

42693953

original gDNA sequence snippet

CCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGG

altered gDNA sequence snippet

CCTGATGCAGAAGAACCGGCAGAAGGACCGGAAGCTAGGGG

original cDNA sequence snippet

CCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGG

altered cDNA sequence snippet

CCTGATGCAGAAGAACCGGCAGAAGGACCGGAAGCTAGGGG

wildtype AA sequence

MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*

mutated AA sequence

MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RQKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*

speed

1.38 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project